Abstract Background: Children with congenital heart problems have an increased incidence (up to 4%) of thrombotic vascular complications, particularly after interventional catheterization procedures that include device implantation. Clopidogrel, a thienopyridine derivative, is a specific platelet aggregation inhibitor. The preferred anti-thrombotic therapy after percutaneous coronary intervention (PCI) with stent placement in adults has evolved from aspirin and systemic anticoagulation with warfarin to dual antiplatelet therapy with aspirin and clopidogrel. Presently, no published data exists on clopidogrel use in children. Objective: The aim of the present study was to report the first experience with clopidogrel therapy for primary and secondary prevention of thrombotic phenomena in children with complex heart disease after interventional cardiac catheterization, and to suggest a dose regimen for a paediatric population. Methods: A retrospective chart review of all infants and children with complex heart disease treated with clopidogrel in the Hospital for Sick Children, Toronto between January 2001 and April 2004. Clopidogrel dosages, duration of therapy, complications and adverse effects in a paediatric population were explored. Results: Fifteen infants and children with congenital and acquired heart disease were treated with clopidogrel (median age 3.5 years; range 6 weeks- 16 years). In 10 of them endovascular stents were inserted. Dosages ranged from 1 to 6 mg/kg/day, for periods ranging between 1 to 6 months. No thrombotic events were reported in these patients during clopidogrel therapy. One child had a bleeding complication (gastrointestinal) while on triple antithrombotic therapy. Other complications reported in adults, such as rash, were not noted in this paediatric series. Conclusion: Clopidogrel was well tolerated, and there were no thrombotic events during treatment. We suggest a dose of 1mg/kg/day for children to be started.